BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231799.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 2,673,955 number of mapped reads = 2,149,787 (80.4%) number of supplementary alignments = 14,473 (0.54%) number of secondary alignments = 0 number of mapped bases = 133,823,474 bp number of sequenced bases = 133,771,507 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 161,683 duplication rate = 2.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7898 >>>>>>> ACTG content number of A's = 38,763,356 bp (28.98%) number of C's = 25,489,063 bp (19.05%) number of T's = 36,213,742 bp (27.07%) number of G's = 33,295,250 bp (24.89%) number of N's = 10,096 bp (0.01%) GC percentage = 43.94% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 915,810 number of insertions = 9,955 mapped reads with insertion percentage = 0.46% number of deletions = 31,260 mapped reads with deletion percentage = 1.44% homopolymer indels = 42.79% >>>>>>> Coverage mean coverageData = 0.0432X std coverageData = 11.8541X There is a 3.63% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 12534088 0.05028708835192832 0.8085056788951477 chr2 243199373 13797266 0.05673232553934257 42.26843001873044 chr3 198022430 13333422 0.06733288749158366 0.2858207350781712 chr4 191154276 4286922 0.022426503292032034 0.18730961242031788 chr5 180915260 6866589 0.03795472532278372 0.21654341028436144 chr6 171115067 10041638 0.05868354070772739 0.3397231951845249 chr7 159138663 8567348 0.053835741978050924 0.6377227428836105 chr8 146364022 7016880 0.04794128983419163 0.6054470697048541 chr9 141213431 5921839 0.04193538077833404 0.3445338916553075 chr10 135534747 6105378 0.045046588680318266 0.38455683422764486 chr11 135006516 4882483 0.0361647951866264 0.34410684105841477 chr12 133851895 5115669 0.038218876169067315 0.22195003804195043 chr13 115169878 4969538 0.04314963327476999 0.22732932288664448 chr14 107349540 4817269 0.044874612411008 0.3662384293407965 chr15 102531392 2183635 0.02129723353409656 0.16649395293468613 chr16 90354753 2971409 0.032886028696243574 0.23811910246322796 chr17 81195210 2828412 0.03483471500350821 0.2259013298841415 chr18 78077248 3263410 0.04179719551590753 0.7364456717693059 chr19 59128983 2572296 0.04350313280375548 0.53392571209345 chr20 63025520 3867962 0.06137136194988951 0.2866878156332026 chr21 48129895 3283848 0.06822886274736314 0.30104571371724675 chr22 51304566 1166900 0.022744564294725735 0.16352830485924497 chrMT 16571 123594 7.458451511677026 5.363676283984319 chrX 155270560 2980517 0.019195635025725417 0.20709456772036722 chrY 59373566 325162 0.00547654489878543 0.11487319952231205